Job ID = 10609089 sra ファイルのダウンロード中... Completed: 583383K bytes transferred in 69 seconds (68690K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 28824750 spots for /home/okishinya/chipatlas/results/dm3/SRX3011227/SRR5834704.sra Written 28824750 spots for /home/okishinya/chipatlas/results/dm3/SRX3011227/SRR5834704.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:20 28824750 reads; of these: 28824750 (100.00%) were unpaired; of these: 353117 (1.23%) aligned 0 times 28026605 (97.23%) aligned exactly 1 time 445028 (1.54%) aligned >1 times 98.77% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9558998 / 28471633 = 0.3357 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 04 May 2018 07:14:49: # Command line: callpeak -t SRX3011227.bam -f BAM -g dm -n SRX3011227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011227.05 # format = BAM # ChIP-seq file = ['SRX3011227.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 04 May 2018 07:14:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:49: # Command line: callpeak -t SRX3011227.bam -f BAM -g dm -n SRX3011227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011227.10 # format = BAM # ChIP-seq file = ['SRX3011227.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 04 May 2018 07:14:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:49: # Command line: callpeak -t SRX3011227.bam -f BAM -g dm -n SRX3011227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011227.20 # format = BAM # ChIP-seq file = ['SRX3011227.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 04 May 2018 07:14:49: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:49: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:55: 1000000 INFO @ Fri, 04 May 2018 07:14:56: 1000000 INFO @ Fri, 04 May 2018 07:14:56: 1000000 INFO @ Fri, 04 May 2018 07:15:02: 2000000 INFO @ Fri, 04 May 2018 07:15:03: 2000000 INFO @ Fri, 04 May 2018 07:15:03: 2000000 INFO @ Fri, 04 May 2018 07:15:09: 3000000 INFO @ Fri, 04 May 2018 07:15:10: 3000000 INFO @ Fri, 04 May 2018 07:15:10: 3000000 INFO @ Fri, 04 May 2018 07:15:16: 4000000 INFO @ Fri, 04 May 2018 07:15:17: 4000000 INFO @ Fri, 04 May 2018 07:15:17: 4000000 INFO @ Fri, 04 May 2018 07:15:22: 5000000 INFO @ Fri, 04 May 2018 07:15:24: 5000000 INFO @ Fri, 04 May 2018 07:15:24: 5000000 INFO @ Fri, 04 May 2018 07:15:29: 6000000 INFO @ Fri, 04 May 2018 07:15:31: 6000000 INFO @ Fri, 04 May 2018 07:15:31: 6000000 INFO @ Fri, 04 May 2018 07:15:36: 7000000 INFO @ Fri, 04 May 2018 07:15:38: 7000000 INFO @ Fri, 04 May 2018 07:15:38: 7000000 INFO @ Fri, 04 May 2018 07:15:42: 8000000 INFO @ Fri, 04 May 2018 07:15:45: 8000000 INFO @ Fri, 04 May 2018 07:15:45: 8000000 INFO @ Fri, 04 May 2018 07:15:49: 9000000 INFO @ Fri, 04 May 2018 07:15:52: 9000000 INFO @ Fri, 04 May 2018 07:15:52: 9000000 INFO @ Fri, 04 May 2018 07:15:56: 10000000 INFO @ Fri, 04 May 2018 07:15:59: 10000000 INFO @ Fri, 04 May 2018 07:15:59: 10000000 INFO @ Fri, 04 May 2018 07:16:02: 11000000 INFO @ Fri, 04 May 2018 07:16:06: 11000000 INFO @ Fri, 04 May 2018 07:16:06: 11000000 INFO @ Fri, 04 May 2018 07:16:09: 12000000 INFO @ Fri, 04 May 2018 07:16:13: 12000000 INFO @ Fri, 04 May 2018 07:16:13: 12000000 INFO @ Fri, 04 May 2018 07:16:16: 13000000 INFO @ Fri, 04 May 2018 07:16:20: 13000000 INFO @ Fri, 04 May 2018 07:16:20: 13000000 INFO @ Fri, 04 May 2018 07:16:22: 14000000 INFO @ Fri, 04 May 2018 07:16:27: 14000000 INFO @ Fri, 04 May 2018 07:16:27: 14000000 INFO @ Fri, 04 May 2018 07:16:29: 15000000 INFO @ Fri, 04 May 2018 07:16:34: 15000000 INFO @ Fri, 04 May 2018 07:16:34: 15000000 INFO @ Fri, 04 May 2018 07:16:36: 16000000 INFO @ Fri, 04 May 2018 07:16:41: 16000000 INFO @ Fri, 04 May 2018 07:16:41: 16000000 INFO @ Fri, 04 May 2018 07:16:42: 17000000 INFO @ Fri, 04 May 2018 07:16:48: 17000000 INFO @ Fri, 04 May 2018 07:16:48: 17000000 INFO @ Fri, 04 May 2018 07:16:49: 18000000 INFO @ Fri, 04 May 2018 07:16:55: 18000000 INFO @ Fri, 04 May 2018 07:16:55: 18000000 INFO @ Fri, 04 May 2018 07:16:55: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:16:55: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:16:55: #1 total tags in treatment: 18912635 INFO @ Fri, 04 May 2018 07:16:55: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:16:56: #1 tags after filtering in treatment: 18912635 INFO @ Fri, 04 May 2018 07:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:56: #1 finished! INFO @ Fri, 04 May 2018 07:16:56: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:57: #2 number of paired peaks: 3378 INFO @ Fri, 04 May 2018 07:16:57: start model_add_line... INFO @ Fri, 04 May 2018 07:16:58: start X-correlation... INFO @ Fri, 04 May 2018 07:16:58: end of X-cor INFO @ Fri, 04 May 2018 07:16:58: #2 finished! INFO @ Fri, 04 May 2018 07:16:58: #2 predicted fragment length is 279 bps INFO @ Fri, 04 May 2018 07:16:58: #2 alternative fragment length(s) may be 279 bps INFO @ Fri, 04 May 2018 07:16:58: #2.2 Generate R script for model : SRX3011227.20_model.r INFO @ Fri, 04 May 2018 07:16:58: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:01: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:17:01: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:17:01: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:17:01: #1 total tags in treatment: 18912635 INFO @ Fri, 04 May 2018 07:17:01: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:17:01: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:01: #1 total tags in treatment: 18912635 INFO @ Fri, 04 May 2018 07:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:17:01: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:17:02: #1 tags after filtering in treatment: 18912635 INFO @ Fri, 04 May 2018 07:17:02: #1 tags after filtering in treatment: 18912635 INFO @ Fri, 04 May 2018 07:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:17:02: #1 finished! INFO @ Fri, 04 May 2018 07:17:02: #1 finished! INFO @ Fri, 04 May 2018 07:17:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:17:03: #2 number of paired peaks: 3378 INFO @ Fri, 04 May 2018 07:17:03: start model_add_line... INFO @ Fri, 04 May 2018 07:17:03: #2 number of paired peaks: 3378 INFO @ Fri, 04 May 2018 07:17:03: start model_add_line... INFO @ Fri, 04 May 2018 07:17:04: start X-correlation... INFO @ Fri, 04 May 2018 07:17:04: end of X-cor INFO @ Fri, 04 May 2018 07:17:04: #2 finished! INFO @ Fri, 04 May 2018 07:17:04: #2 predicted fragment length is 279 bps INFO @ Fri, 04 May 2018 07:17:04: #2 alternative fragment length(s) may be 279 bps INFO @ Fri, 04 May 2018 07:17:04: #2.2 Generate R script for model : SRX3011227.05_model.r INFO @ Fri, 04 May 2018 07:17:04: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:04: start X-correlation... INFO @ Fri, 04 May 2018 07:17:04: end of X-cor INFO @ Fri, 04 May 2018 07:17:04: #2 finished! INFO @ Fri, 04 May 2018 07:17:04: #2 predicted fragment length is 279 bps INFO @ Fri, 04 May 2018 07:17:04: #2 alternative fragment length(s) may be 279 bps INFO @ Fri, 04 May 2018 07:17:04: #2.2 Generate R script for model : SRX3011227.10_model.r INFO @ Fri, 04 May 2018 07:17:04: #3 Call peaks... INFO @ Fri, 04 May 2018 07:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:18:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:12: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:13: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:31: #4 Write output xls file... SRX3011227.20_peaks.xls INFO @ Fri, 04 May 2018 07:18:31: #4 Write peak in narrowPeak format file... SRX3011227.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:31: #4 Write summits bed file... SRX3011227.20_summits.bed INFO @ Fri, 04 May 2018 07:18:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6314 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:38: #4 Write output xls file... SRX3011227.10_peaks.xls INFO @ Fri, 04 May 2018 07:18:38: #4 Write peak in narrowPeak format file... SRX3011227.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:39: #4 Write summits bed file... SRX3011227.10_summits.bed INFO @ Fri, 04 May 2018 07:18:39: Done! pass1 - making usageList (13 chroms): 3 millis INFO @ Fri, 04 May 2018 07:18:39: #4 Write output xls file... SRX3011227.05_peaks.xls pass2 - checking and writing primary data (10002 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:39: #4 Write peak in narrowPeak format file... SRX3011227.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:39: #4 Write summits bed file... SRX3011227.05_summits.bed INFO @ Fri, 04 May 2018 07:18:39: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (13351 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。